Molecular Phylogenetics and Evolution xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution ⁎ Catriona Munroa, ,1, Stefan Sieberta,b,1, Felipe Zapatac, Mark Howisond,e, Alejandro Damian-Serranoa,j, Samuel H. Churcha,f, Freya E. Goetza,g, Philip R. Pughh, Steven H.D. Haddocki, Casey W. Dunnj a Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA b Department of Molecular & Cellular Biology, University of California Davis, Davis, CA 95616, USA2 c Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA d Brown Data Science Practice, Brown University, Providence, RI 02912, USA e Watson Institute for International and Public Affairs, Brown University, Providence, RI 02912, USA2 f Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA2 g Smithsonian Institution, National Museum of Natural History, Washington, DC 20560, USA2 h National Oceanography Centre, Southampton SO14 3ZH, UK i Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA j Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA ABSTRACT Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at most depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. They play important roles in ocean eco- systems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups. There was, however, little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 29 siphonophore species analyzed in combi- nation with 14 publicly available genomic and transcriptomic datasets. We use this new phylogeny to re- construct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose at least twice. 1. Introduction length (Mackie et al., 1987). There is also a small clade of benthic si- phonophores, Rhodaliidae, that are tethered to the bottom for part of Siphonophores (Figs. 1 and 2) are among the most abundant gela- their lives (Pugh, 1983). There are currently 187 valid described si- tinous predators in the open ocean, and have a large impact on ocean phonophore species (Schuchert, 2018). ecosystems (Choy et al., 2017; Pagès et al., 2001; Pugh, 1984; Pugh Siphonophores remain poorly known, in large part because they are et al., 1997; Purcell, 1981; Williams and Conway, 1981). Siphono- fragile and difficult to collect. They have, however, been of great in- phores, which belong to Hydrozoa (Cnidaria), are found at most depths terest for more than 150 years due to their unique structure and de- in the ocean, with the deepest recorded species found around 4,300 m velopment (Mackie et al., 1987; Mapstone, 2014). Like many other (Lindsay, 2005). The most familiar species is the Portuguese man of war cnidarians, they are colonial: they grow by incomplete asexual re- Physalia physalis, which floats at the surface and can wash up con- production. Each colony arises from a single embryo that forms the spicuously onto beaches (Totton, 1960). Most species are planktonic, protozooid, the first body. One or two growth zones (Fig. 2) then arise living in the water column, where some grow to be more than 30 m in and asexually produce other genetically identical zooids that remain ⁎ Corresponding author. E-mail address: [email protected] (C. Munro). 1 Authors contributed equally. 2 Current address. https://doi.org/10.1016/j.ympev.2018.06.030 Received 28 January 2018; Received in revised form 19 May 2018; Accepted 18 June 2018 1055-7903/ © 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/BY/4.0/). Please cite this article as: Munro, C., Molecular Phylogenetics and Evolution (2018), https://doi.org/10.1016/j.ympev.2018.06.030 C. Munro et al. Molecular Phylogenetics and Evolution xxx (xxxx) xxx–xxx Fig. 1. Photographs of living siphonophores. Colored circles correspond to the clades shown in Fig. 3 as follows: Cystonectae (A and B), Ca- lycophorae (C–G), Apolemiidae (H), and Clade A within Euphysonectae (I-K). (A) Rhizophysa ey- senhardtii, scale bar = 1 cm. (B) Bathyphysa con- ifera, scale bar = 2 cm. (C) Hippopodius hippopus, scale bar = 5 mm. (D) Kephyes hiulcus, scale bar = 2 mm. (E) Desmophyes haematogaster, scale bar = 5 mm. (F) Sphaeronectes christiansonae, scale bar = 2 mm. (G) Praya dubia, scale bar = 4 cm. (H) Apolemia sp., scale bar = 1 cm. (I) Lychnagalma utricularia, scale bar = 1 cm. (J) Nanomia sp., scale bar = 1 cm. (K) Physophora hydrostatica, scale bar = 5 mm. Photo credits: S. Siebert (C,H,I,K), S. Haddock (A,D,E,F), R. Sherlock (B), MBARI (G), C. Munro (J). (For in- terpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) attached (Carré, 1967, 1969; Carré and Carré, 1991, 1993). In some within “Physonectae”. The name Codonophora was given to this clade species additional zooids are added outside the growth zone along the of “Physonectae” and Calycophorae (Dunn et al., 2005). siphosomal stem (Siebert et al., 2013). The zooids are each homologous Major questions remained after this early work, though. In parti- to a solitary animal, but are physiologically integrated (Dunn and cular, there was little support for important deep relationships within Wagner, 2006; Mackie et al., 1987; Totton, 1965). Siphonophores differ Codonophora. Understanding these relationships is key to resolving the significantly from other colonial animals in their colony structure and evolution of several traits of importance, including sexual systems development – their zooids are highly functionally specialized and ar- (monoecy versus dioecy) and the gain and loss of particular zooids, ranged in precise, repeating, species-specific patterns (Beklemishev, such as palpons (Fig. 2). Here we present a broadly sampled phyloge- 1969; Cartwright and Nawrocki, 2010). Zooids are specialized for a netic analysis of Siphonophora that considers transcriptomic data from range of functions, including feeding, reproduction, or swimming 33 siphonophore species and 10 outgroup species (2 outgroups were (Fig. 2)(Dunn and Wagner, 2006). subsequently excluded due to poor sampling). Using 1,423 genes, we Understanding the unique ecology, morphology, and development find strong support for many relationships found in the earlier phylo- of siphonophores requires a well-resolved phylogeny of the group. The geny (Dunn et al., 2005), and also provide new resolution for key re- relationship of siphonophores to other hydrozoans has been difficult to lationships that were unresolved in that previous study. Using this determine (Cartwright et al., 2008; Cartwright and Nawrocki, 2010; phylogeny, we reconstruct the evolutionary history of characters cen- Kayal et al., 2013, 2015, 2018; Zapata et al., 2015), but there has been tral to the unique biology of siphonophores, including zooid type, life progress on their internal relationships. A phylogeny (Dunn et al., history traits, and vertical habitat use. 2005) based on two genes (16S, 18S) from 52 siphonophore taxa ad- dressed several long standing questions about siphonophore biology, including the relationships of the three historically recognized groups, 2. Material and methods Cystonectae, Physonectae, and Calycophorae. Cystonectae was found to be sister to all other siphonophores, while Calycophorae were nested All scripts for the analyses are available in a git repository at https://github.com/caseywdunn/siphonophore_ phylogeny_2017. The 2 C. Munro et al. Molecular Phylogenetics and Evolution xxx (xxxx) xxx–xxx (Zymo #R1050), or from total RNA after Trizol (Ambion, #15596026) extraction and through purification using Dynabeads mRNA Purification Kit (Ambion, #61006). In case of small total RNA quan- tities, only a single round of bead purification was performed. Extractions were performed according to the manufacturer’s instruc- tion. All samples were DNase treated (TURBO DNA-free, Invitrogen #AM1907; or on column DNase treatment with Zymo Quick RNA MicroPrep). Libraries were prepared for sequencing using the Illumina TruSeq RNA Sample Prep Kit (Illumina, #FC-122-1001, #FC-122- 1002), the Illumina TruSeq Stranded Library Prep Kit (Illumina, #RS- 122-2101) or the NEBNext RNA Sample Prep Master Mix Set (NEB, #E6110S). We collected long read paired end Illumina data for de novo transcriptome assembly. In the case of large tissue inputs, libraries were sequenced separately for each tissue, subsequently subsampled and pooled in silico. Libraries were sequenced on the HiSeq 2000, 2500, and 3000 sequencing platforms. Summary statistics for each library are given